Firstly, welcome to our discussion forum and thanks for reporting us these missing values in the SIM-XL output file.
Actually, when the xl schema was developed (at the beginning of last year) both attributes ('start' and 'end') were optional even to cross-linking results, however, after to release the final version they turned required except to de novo.
However, we agree with you and we updated our SIM-XL results inserting these attributes ('start' and 'end' on PeptideEvidence tag).
We've released a new version of the SIM-XL (v. 1.5.1.3) with this update.
The following messages were obtained during the validation of your XML file:
Message 1:
Rule ID: CvListObjectRule
Level: INFO
Context(/MzIdentML/cvList )
--> The cv element for PSI-MS uses an old version.
Tip: Provide the newest version for all cv element under the CvList element./MzIdentML/cvList
Message 2:
Rule ID: SpectrumIdentificationList_may_rule
Level: INFO
Context(/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/cvParam/@accession' because no values were found:
- Any children term of MS:1001184 (search statistics). The term can be repeated. The matching value has to be the identifier of the term, not its name.
Message 3:
Rule ID: DBSequence_ProteinDescription_may_rule
Level: INFO
Context(/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/SequenceCollection/DBSequence/cvParam/@accession' because no values were found:
- The sole term MS:1001088 (protein description) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
Message 4:
Rule ID: SearchDatabase_may_rule
Level: INFO
Context(/searchDatabase/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/Inputs/searchDatabase/cvParam/@accession' because no values were found:
- Any children term of MS:1001011 (search database details). The term can be repeated. The matching value has to be the identifier of the term, not its name.
- Any children term of MS:1000561 (data file checksum type). The term can be repeated. The matching value has to be the identifier of the term, not its name.
Message 5:
Rule ID: DBSequence_may_rule
Level: INFO
Context(/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/SequenceCollection/DBSequence/cvParam/@accession' because no values were found:
- Any children term of MS:1001089 (molecule taxonomy). The term can be repeated. The matching value has to be the identifier of the term, not its name.
- Any children term of MS:1001342 (database sequence details). The term can be repeated. The matching value has to be the identifier of the term, not its name.
- Any children term of MS:1002636 (proteogenomics attribute). The term can be repeated. The matching value has to be the identifier of the term, not its name.
Message 6:
Rule ID: SourceFile_may_rule
Level: INFO
Context(/sourceFile/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/Inputs/sourceFile/cvParam/@accession' because no values were found:
- Any children term of MS:1000561 (data file checksum type). The term can be repeated. The matching value has to be the identifier of the term, not its name.
Message 7:
Rule ID: SearchDatabaseDatabaseName_may_rule
Level: INFO
Context(/searchDatabase/databaseName/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/Inputs/searchDatabase/databaseName/cvParam/@accession' because no values were found:
- Any children term of MS:1001013 (database name). The term can be repeated. The matching value has to be the identifier of the term, not its name.
Message 8:
Rule ID: SpectrumIdentificationResult_may_rule
Level: INFO
Context(/spectrumIdentificationResult/cvParam/@accession ) in 248 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/spectrumIdentificationResult/cvParam/@accession' because no values were found:
- The sole term MS:1000894 (retention time) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
- Any children term of MS:1001405 (spectrum identification result details). The term can be repeated. The matching value has to be the identifier of the term, not its name.
======== RULE STATISTICS ========
Invalid XML schema validation: 0
CvMappingRule total count: 50
CvMappingRules not run: 5
CvMappingRules run & not matching: 7
CvMappingRules invalid XPath: 0
CvMappingRules run & valid: 38
ObjectRules total count: 15
ObjectRules not run: 2
ObjectRules run & not matching: 1
ObjectRules run & valid: 12
Unanticipated CV terms: 0
XL interaction scoring messages: 0
Not matching messages received: 7